CCR5_CellScreen

CCR5_CellScreen_1 - Pre-processing

Sample annotation

1 2 3 4 5 6 7 8 9 10 11 12
A MDAMB468 - WT - 1 - Fixed+Tween - NT.fcs

MDAMB468

WT

Fixed+Tween

1

NT
MCF7 - WT - 1 - Fixed+Tween - NT.fcs

MCF7

WT

Fixed+Tween

1

NT
SW480 - WT - 1 - Fixed+Tween - NT.fcs

SW480

WT

Fixed+Tween

1

NT
SW620 - WT - 1 - Fixed+Tween - NT.fcs

SW620

WT

Fixed+Tween

1

NT
HCT116 - WT - 1 - Fixed+Tween - NT.fcs

HCT116

WT

Fixed+Tween

1

NT
HT29 - WT - 1 - Fixed+Tween - NT.fcs

HT29

WT

Fixed+Tween

1

NT
A549 - WT - 1 - Fixed+Tween - NT.fcs

A549

WT

Fixed+Tween

1

NT
H1975 - WT - 1 - Fixed+Tween - NT.fcs

H1975

WT

Fixed+Tween

1

NT
TCV2 - WT - 1 - Fixed+Tween - NT.fcs

TCV2

WT

Fixed+Tween

1

NT
H2052-484 - WT - 1 - Fixed+Tween - NT.fcs

H2052-484

WT

Fixed+Tween

1

NT
B MDAMB468 - WT - 2 - Fixed+Tween - NT.fcs

MDAMB468

WT

Fixed+Tween

2

NT
MCF7 - WT - 2 - Fixed+Tween - NT.fcs

MCF7

WT

Fixed+Tween

2

NT
SW480 - WT - 2 - Fixed+Tween - NT.fcs

SW480

WT

Fixed+Tween

2

NT
SW620 - WT - 2 - Fixed+Tween - NT.fcs

SW620

WT

Fixed+Tween

2

NT
HCT116 - WT - 2 - Fixed+Tween - NT.fcs

HCT116

WT

Fixed+Tween

2

NT
HT29 - WT - 2 - Fixed+Tween - NT.fcs

HT29

WT

Fixed+Tween

2

NT
A549 - WT - 2 - Fixed+Tween - NT.fcs

A549

WT

Fixed+Tween

2

NT
H1975 - WT - 2 - Fixed+Tween - NT.fcs

H1975

WT

Fixed+Tween

2

NT
TCV2 - WT - 2 - Fixed+Tween - NT.fcs

TCV2

WT

Fixed+Tween

2

NT
H226 - WT - 2 - Fixed+Tween - NT.fcs

H226

WT

Fixed+Tween

2

NT
H2052-484 - WT - 2 - Fixed+Tween - NT.fcs

H2052-484

WT

Fixed+Tween

2

NT
C MDAMB468 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

MDAMB468

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
SW480 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

SW480

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
SW620 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

SW620

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
HCT116 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

HCT116

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
HT29 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

HT29

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
A549 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

A549

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
H1975 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H1975

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
TCV2 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

TCV2

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
H226 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H226

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
H2052-484 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H2052-484

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
D MDAMB468 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

MDAMB468

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
MCF7 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

MCF7

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
SW480 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

SW480

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
SW620 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

SW620

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
HCT116 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

HCT116

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
HT29 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

HT29

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
A549 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

A549

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
H1975 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H1975

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
TCV2 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

TCV2

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
H226 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H226

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
H2052-484 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H2052-484

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
E H28 - WT - 1 - Fixed+Tween - NT.fcs

H28

WT

Fixed+Tween

1

NT
ZL34 - WT - 1 - Fixed+Tween - NT.fcs

ZL34

WT

Fixed+Tween

1

NT
ONE58 - WT - 1 - Fixed+Tween - NT.fcs

ONE58

WT

Fixed+Tween

1

NT
211H - WT - 1 - Fixed+Tween - NT.fcs

211H

WT

Fixed+Tween

1

NT
PC3 - WT - 1 - Fixed+Tween - NT.fcs

PC3

WT

Fixed+Tween

1

NT
LNCAP - WT - 1 - Fixed+Tween - NT.fcs

LNCAP

WT

Fixed+Tween

1

NT
DU145 - WT - 1 - Fixed+Tween - NT.fcs

DU145

WT

Fixed+Tween

1

NT
A431 - WT - 1 - Fixed+Tween - NT.fcs

A431

WT

Fixed+Tween

1

NT
LUCA-1 - WT - 1 - Fixed+Tween - NT.fcs

LUCA-1

WT

Fixed+Tween

1

NT
LUCA-62 - WT - 1 - Fixed+Tween - NT.fcs

LUCA-62

WT

Fixed+Tween

1

NT
U87 - WT - 1 - Fixed+Tween - NT.fcs

U87

WT

Fixed+Tween

1

NT
F H28 - WT - 2 - Fixed+Tween - NT.fcs

H28

WT

Fixed+Tween

2

NT
ONE58 - WT - 2 - Fixed+Tween - NT.fcs

ONE58

WT

Fixed+Tween

2

NT
211H - WT - 2 - Fixed+Tween - NT.fcs

211H

WT

Fixed+Tween

2

NT
PC3 - WT - 2 - Fixed+Tween - NT.fcs

PC3

WT

Fixed+Tween

2

NT
LNCAP - WT - 2 - Fixed+Tween - NT.fcs

LNCAP

WT

Fixed+Tween

2

NT
DU145 - WT - 2 - Fixed+Tween - NT.fcs

DU145

WT

Fixed+Tween

2

NT
LUCA-1 - WT - 2 - Fixed+Tween - NT.fcs

LUCA-1

WT

Fixed+Tween

2

NT
LUCA-62 - WT - 2 - Fixed+Tween - NT.fcs

LUCA-62

WT

Fixed+Tween

2

NT
U87 - WT - 2 - Fixed+Tween - NT.fcs

U87

WT

Fixed+Tween

2

NT
G H2452 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H2452

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
H28 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H28

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
ZL34 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

ZL34

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
ONE58 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

ONE58

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
211H - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

211H

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
PC3 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

PC3

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
LNCAP - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

LNCAP

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
DU145 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

DU145

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
A431 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

A431

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
LUCA-1 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

LUCA-1

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
LUCA-62 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

LUCA-62

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
U87 - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

U87

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
H H28 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

H28

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
ZL34 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

ZL34

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
ONE58 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

ONE58

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
211H - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

211H

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
PC3 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

PC3

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
LNCAP - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

LNCAP

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
DU145 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

DU145

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
A431 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

A431

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
LUCA-1 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

LUCA-1

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
LUCA-62 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

LUCA-62

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
U87 - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

U87

WT

Fixed+Tween

2

aCCR5-Hek/1/85a

Data cleaning

Raw data

Raw data, FSC-A vs SSC-A

Outlier cleaning

Outlier cleaning, FSC-A vs SSC-A

Main cell population gating

FSC-A vs SSC-A, Main cell population gating

FSC-A vs SSC-A, Main cell population gated

Singlets cleaning, SSC

SSC-A vs SSC-H, SSC singlet gating

SSC-A vs SSC-H, SSC singlets gated

FSC-A vs SSC-A, SSC singlets gated

Singlets cleaning, FSC

FSC-A vs SSC-A, FSC singlet gating

FSC-A vs FSC-H, FSC singlet gating

FSC-A vs SSC-A, FSC singlet gated

Cleaned dataset

Cleaned dataset, FSC-A vs SSC-A

Cleaned dataset, Missing samples removed, FSC-A vs SSC-A

CCR5_CellScreen_2 - Pre-processing

Sample annotation

1 2 3 4
A CHO - WT - 1 - Live - NT.fcs

CHO

WT

Live

1

NT
CHO - CCR5 - 1 - Live - NT.fcs

CHO

CCR5

Live

1

NT
HEK - WT - 1 - Live - NT.fcs

HEK

WT

Live

1

NT
HEK - CCR5 - 1 - Live - NT.fcs

HEK

CCR5

Live

1

NT
B CHO - CCR5 - 2 - Live - NT.fcs

CHO

CCR5

Live

2

NT
HEK - WT - 2 - Live - NT.fcs

HEK

WT

Live

2

NT
HEK - CCR5 - 2 - Live - NT.fcs

HEK

CCR5

Live

2

NT
C CHO - WT - 1 - Live - CCR5-Hek-1-85a.fcs

CHO

WT

Live

1

aCCR5-Hek/1/85a
CHO - CCR5 - 1 - Live - CCR5-Hek-1-85a.fcs

CHO

CCR5

Live

1

aCCR5-Hek/1/85a
HEK - WT - 1 - Live - CCR5-Hek-1-85a.fcs

HEK

WT

Live

1

aCCR5-Hek/1/85a
HEK - CCR5 - 1 - Live - CCR5-Hek-1-85a.fcs

HEK

CCR5

Live

1

aCCR5-Hek/1/85a
D CHO - CCR5 - 2 - Live - CCR5-Hek-1-85a.fcs

CHO

CCR5

Live

2

aCCR5-Hek/1/85a
HEK - WT - 2 - Live - CCR5-Hek-1-85a.fcs

HEK

WT

Live

2

aCCR5-Hek/1/85a
HEK - CCR5 - 2 - Live - CCR5-Hek-1-85a.fcs

HEK

CCR5

Live

2

aCCR5-Hek/1/85a
E CHO - WT - 1 - Fixed+Tween - NT.fcs

CHO

WT

Fixed+Tween

1

NT
HEK - CCR5 - 1 - Fixed+Tween - NT.fcs

HEK

CCR5

Fixed+Tween

1

NT
F CHO - WT - 2 - Fixed+Tween - NT.fcs

CHO

WT

Fixed+Tween

2

NT
CHO - CCR5 - 2 - Fixed+Tween - NT.fcs

CHO

CCR5

Fixed+Tween

2

NT
HEK - CCR5 - 2 - Fixed+Tween - NT.fcs

HEK

CCR5

Fixed+Tween

2

NT
G CHO - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

CHO

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
CHO - CCR5 - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

CHO

CCR5

Fixed+Tween

1

aCCR5-Hek/1/85a
HEK - WT - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

HEK

WT

Fixed+Tween

1

aCCR5-Hek/1/85a
HEK - CCR5 - 1 - Fixed+Tween - CCR5-Hek-1-85a.fcs

HEK

CCR5

Fixed+Tween

1

aCCR5-Hek/1/85a
H CHO - WT - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

CHO

WT

Fixed+Tween

2

aCCR5-Hek/1/85a
CHO - CCR5 - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

CHO

CCR5

Fixed+Tween

2

aCCR5-Hek/1/85a
HEK - CCR5 - 2 - Fixed+Tween - CCR5-Hek-1-85a.fcs

HEK

CCR5

Fixed+Tween

2

aCCR5-Hek/1/85a

Data cleaning

Raw data

Raw data, FSC-A vs SSC-A

Outlier cleaning

Outlier cleaning, FSC-A vs SSC-A

Main cell population gating

FSC-A vs SSC-A, Main cell population gating

FSC-A vs SSC-A, Main cell population gated

Singlets cleaning, SSC

SSC-A vs SSC-H, SSC singlet gating

SSC-A vs SSC-H, SSC singlets gated

FSC-A vs SSC-A, SSC singlets gated

Singlets cleaning, FSC

FSC-A vs SSC-A, FSC singlet gating

FSC-A vs FSC-H, FSC singlet gating

FSC-A vs SSC-A, FSC singlet gated

Cleaned dataset

Cleaned dataset, FSC-A vs SSC-A

Cleaned dataset, Missing samples removed, FSC-A vs SSC-A

Data analysis

Data analysis, density plots

APC probe & cell mutation comparisons, APC-A

-1

Data analysis, bar graphs

APC probe & cell mutation comparisons, APC-A, Median fluorescence intensity

-1

Data analysis, interactive bar graphs

APC probe & cell mutation comparisons, APC-A, Median fluorescence intensity

-1

Data analysis, Data tables

Data table, Event analysis

Data table, individual replicates, long

Data table, individual replicates, wide

Data table, Statistics, long

Analysis parameters

Variable name Variable description Choice for the analysis
parameter_analysis_title Name of your analysis CCR5_CellScreen
parameter_channels_to_display Channels to display APC-A
parameter_comparisons_to_make_primary Which parameters do you want to display the flow cytometry density plots on the same graphs (the other will be facets) (colors) APC_probe
parameter_comparisons_to_make_secondary Which parameters do you want to display the flow cytometry density plots on the same graphs (the other will be facets) (linetype) cell_mutation
parameter_entity_of_interest Which parameter do you want as the x axis of the bar graphs ? sample
parameter_facets_to_remove Which parameters do you want not to be included in the facets template_name, sample
parameter_free_y Type of scale for the density plots free_y
parameter_gate_preset_fscsscs Use a preset for the debris and main cloud gating on FSC and SSC ? (Will overide manually defined windows) gate_preset_fscssc_cho
parameter_individual_trace_graphs Data cleaning to perform main_cell_pop_enabled, fsc_singlet_enabled, ssc_singlet_enabled
parameter_ncol_density_plots Number of graphs in each columns for the density plots 3
parameter_output_graphs Output non-interactive graphs ? TRUE
parameter_process_from_script Used to check if reporting was started from a script. Do not change. FALSE
parameter_quantile_value_ceiling Quantile ceiling for graphs 0.9999
parameter_quantile_value_floor Quantile floor for graphs 0.01
parameter_radius_cloud Multiplier for the radius of the main population selection (try 2.5 for PBMCs) 1.5
parameter_remove_empty After gating, remove the samples that do not have an annotation in these categories comments_1, placeholder
parameter_scale_density Normalize the density plot maximum to 1? FALSE
parameter_single_dataset_name For batch processing. Do not modify DrugDisc
parameter_theme_density_plots Theme for the density plots ? (check https://ggplot2.tidyverse.org/reference/ggtheme.html for exemples) theme_gray
parameter_window_debris Approximate boundaries for the debris separated by semicolumns (SSC-A_floor;SSC-A_ceiling;FSC-A_floor;FSC-A_ceiling) (OPTIONAL)
parameter_window_of_interest Approximate boundaries of the population of interest separated by semicolumns (SSC-A_floor;SSC-A_ceiling;FSC-A_floor;FSC-A_ceiling) (OPTIONAL) 0;1e60;1e6;1e15